Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses.

Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of principal component (DAPC) and model-based method (STRUCTURE) were employed. The results of the population analysis clearly demonstrated a distinct separation of native and exotic horse breeds and clarified the relationships between studied breeds. The effective population size (Ne) for the last six generations was estimated 54, 49, 37, 35, 27 and 26 for the Caspian, Kurdish, Arabian, Turkmen, Akhal-Teke and Fell pony breeds, respectively. The Caspian breed showed the lowest LD with an average r2 value of 0.079, while the highest was observed in Fell pony (0.148). The highest and lowest average observed heterozygosity were found in the Kurdish breeds (0.346) and Fell pony (0.290) breeds, respectively. The lowest genomic inbreeding coefficient based on run of homozygosity (FROH) and excess of homozygosity (FHOM) was in the Caspian and Kurdish breeds, respectively, while based on genomic relationship matrix) FGRM) and correlation between uniting gametes) FUNI) the lowest genomic inbreeding coefficient was found in the Kurdish breed. The estimation of genomic inbreeding rates in the six breeds revealed that FROH yielded lower estimates compared to the other three methods. Additionally, the Iranian breeds displayed lower levels of inbreeding compared to the exotic breeds. Overall, the findings of this study provide valuable insights for the development of effective breeding management strategies aimed at preserving these horse breeds.

A meta-analysis on association between CSN3 gene variants and milk yield and composition in cattle.

A meta-analysis on the effects of A and B alleles, the most frequent alleles of CSN3 gene, on milk yield and composition traits was conducted by pooling a large dataset consisting of 30 471 genotyped cattle. Four genetic models, comprising dominant (AA + AB vs. BB), recessive (AA vs. AB + BB), additive (AA vs. BB) and co-dominant (AA + BB vs. AB), were employed to analyze data. Standardized mean difference (SMD) was used to measure the size of the effects of A and B alleles of CSN3 on studied traits. Effect sizes of 0.2, 0.5 and 0.8 represent small, medium and large effects, respectively. The results indicate that B allele, in the form of BB genotype, has a significant, but medium effect on lactation yield under dominant (SMD = 0.259, P-value = 0.006) and additive (SMD = 0.279, P-value = 0.035) models. Moreover, a small decrease in the fat percentage occurred in cows having A allele under dominant (SMD = -0.077, P-value = 0.006) and additive (SMD = -0.106, P-value = 0.035) models. Furthermore, CSN3 variants significantly but slightly affect protein percentage under dominant (SMD = -0.146, P-value = 0.000), recessive (SMD = -0.077, P-value = 0.000) and additive (SMD = -0.219, P-value = 0.000) models, showing the negative effect of A allele on this trait. Meta-analysis results reveal that daily milk yield is slightly affected by CSN3 variants under recessive (SMD = 0.056, P-value = 0.033) and additive (SMD = 0.061, P-value = 0.013) genetic models. There is no effect of CSN3 variants on either protein or fat yield. In addition, the effects of CSN3 variants on milk-related traits were not observed under the co-dominant model. Sensitivity and publication bias analyses were carried out to confirm the stability of meta-analyses results.

Effect of a high dose of exogenous phytase and supplementary myo-inositol on mineral solubility of broiler digesta and diets subjected to in vitro digestion assay.

This study was conducted to evaluate the effect of microbial phytase and myo-inositol supplementation in low non-phytate phosphorus (nPP) diets on pH and the solubility of minerals in an in vitro digestion procedure (IVDP) and to compare this with digesta from birds fed different diets (grower diets) compared to the in vitro test (starter diets). A total of 660 1-day-old broilers were randomly allotted into 11 dietary treatments and fed a corn-soybean-meal-based diet with recommended nPP (positive control; PC), an nPP-deficient diet (negative control; NC), NC diets supplemented with phytase (500; 1,000; 2,000; 3,000; 4,000; 5,000; and 6,000 FTU/kg), an NC diet plus 0.15% myo-inositol, and an NC diet with reduced Ca level (Ca: nPP ratio same as PC) from 1 to 23 D of age. The pH and Ca solubility of the NC diet was increased compared with the PC when subjected to IVDP (P < 0.05). P solubility in the gizzard and jejunal digesta was reduced in the NC compared with the PC diet and this was also reflected in the IVDP. Phytase addition to the NC diets linearly increased (P < 0.05) the pH value and Ca and P solubilities in both digesta and diets subjected to IVDP. Higher doses of microbial phytase increased (P < 0.05) Zn and Fe solubilities in both digesta and IVDP. Myo-inositol supplementation of the NC diet had no effect on mineral solubility, but decreased (P < 0.05) the pH of the IVDP. Lowering the Ca content of the NC diet decreased (P < 0.05) the pH of the in vitro digested diets and Ca solubility in both broiler digesta and IVDP and also increased (P < 0.05) P solubility in both the jejunal digesta and IVDP. Correlations were noted between the solubility of P in the in vitro assay and that in the gizzard and jejunal digesta, and also with bird performance, confirms the usefulness of in vitro assay.

Increased sperm cell production in ageing roosters by an oral treatment with an aromatase inhibitor and a natural herbal extract designed for improving fertility.

Rooster fertility peaks between 30 and 40 weeks of age and declines rapidly from 50 weeks of age. This is linked to a reduction in the number of spermatozoa in the ejaculate due to high density of spermatids in the seminiferous tubules of low-fertility roosters. In this study, we assessed the effects over spermatogenesis of both letrozole, an aromatase inhibitor, and a commercial herbal extract designed for improving fertility composed by Tribulus, Cinnamomum, Zingiber and Sativus. Forty-two-week-old Ross 308 roosters (n = 24) were distributed into four groups: control, letrozole (0.03 mg/kg), herbal extract (0.04 ml/kg) and letrozole+herbal extract. After 14 weeks of daily oral supplementation, their testes and epididymides were weighed, fixed and sectioned for assessment of spermatogenesis and quantification of sperm cells inside the lumen. Differences in seminiferous tubules measurements and density of sperm cells were tested using R software (version 3.0.1). Although body weight was not affected by the treatment, testes from animals treated with the combination of letrozole and herbal extracts were heavier than those from control animals. Animals treated with either letrozole or herbal extract, or their combination, showed a significant higher number of sperm cells inside the seminiferous tubules and epididymis than control animals (p < .05). These data suggest that the use of letrozole and the herbal extract could improve sperm cell production in ageing roosters. Future studies are needed to disclose the causal mechanisms involved and its effect on fertility and ejaculate features.

Effects of a high dose of microbial phytase and myo-inositol supplementation on growth performance, tibia mineralization, nutrient digestibility, litter moisture content, and foot problems in broiler chickens fed phosphorus-deficient diets.

A total of 660 one-day-old Ross 308 broiler chicks were randomly distributed into eleven dietary treatments. Treatments included a maize-soybean meal-based diet with recommended calcium (Ca) and non-phytate phosphorus (nPP) (positive control; PC), an nPP-deficient diet (negative control; NC), NC diets supplemented with different levels of phytase (0, 500, 1,000, 2,000, 3,000, 4,000, 5,000, and 6,000 FTU/kg), a NC diet plus 0.15% myo-inositol, and a NC diet with reduced Ca level (Ca to nPP ratio same as PC). Feeding the NC diet had no effects on birds' body weight (BW), weight gain (WG), feed intake (FI), and feed conversion ratio (FCR), but decreased (P < 0.05) tibia P contents, crude protein (CP) digestibility, and serum P, but increased (P < 0.05) serum alkaline phosphatase (ALP) activity at 21 d of age. Phytase supplementation at ≥4,000 FTU/kg improved (P < 0.05) BW, WG and digestibility of nutrients. Feeding the NC diet resulted in greater (P < 0.05) litter moisture content (42 d) and poorer gait score (21 d), but 4,000 and 6,000 FTU/kg phytase returned (P < 0.05) these parameters to that of the PC. Supplemental myo-inositol increased (P < 0.05) serum total protein, P retention, and decreased (P < 0.05) litter moisture at 42 d of age. Feeding the low Ca NC diet increased (P < 0.05) serum total protein, ileum Ca, P, and CP digestibility and decreased serum ALP activity, litter moisture and gait score compared to the NC group. In conclusion, phytase in a dose-dependent manner, especially at ≥4,000 FTU/kg levels, was effective in overcoming the negative consequences of NC diets, primarily due to the ability to improve nutrient utilization. In addition, reducing the Ca level or supplementation of inositol of NC diet can correct some the negative effects of feeding a NC diet confirming the negative effect of a wide Ca: P ratio in a P-deficient diet and suggesting that inositol may play a role in the response to phytase addition.

Cholestasis induced antinociception and decreased gene expression of MOR1 in rat brain.

We examined antinociception and gene expression of mu-opioid receptor 1 (MOR1) in some brain areas of cholestatic rats, 21 days after common bile duct ligation (BDL). Cholestasis was induced in male Wistar rats during laparotomy and common BDL. Pain behavior was assessed on days 7, 14 or 21 of BDL using a hotplate test in control, sham and cholestatic groups. On day 21 of BDL, other groups of rats were sacrificed, whole brains were extracted, and the hypothalamus, prefrontal cortex (PFC), hippocampus and striatum in control, sham and cholestatic rats were dissected. We used a semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) method for evaluating MOR1 gene expression. The results revealed that cholestatic rats showed significant antinociception on days 14 and 21 of ligation with the most significant effect on day 21, which was prevented by naloxone (1 mg/kg). On the other hand, the expression of MOR1 gene compared to the sham group was decreased by 42% in the hypothalamus, 41% in the PFC, and 67% in the hippocampus after 21 days of BDL, while no significant change in its expression in the striatum was observed. It can be concluded that a change in endogenous opioid levels and its subsequent influence on the gene expression of MOR in some areas of the rat brain may underlie the altered nociception and other possible pathological changes such as pruritus after induction of cholestasis.

Genetic diversity in mazandaranian native cattle: a comparison with Holstein cattle, using ISSR marker.

This study was carried out to investigate genetic diversity in Mazandaranian native cattle population comparised to the Holstein breed, using Inter Simple Sequence Repeats (ISSR) marker. A total of 175 animals, including 71 native and 104 cattle of Holstein breed were screened. The extraction of DNA samples were carried out, using modified salting out method. A 19-mer oligonucleotide, (GA)9C, was used as primer in PCR reactions. The PCR products showed 15 different fragments with length ranged from 120 to 1600 bp in the two breeds.. Genetic variation indexes, including effective number of alleles, Shannon index, Nei's gene diversity and standard genetic distance were estimated, using POPGene software. Generally, the estimated genetic variation indexes showed low levels of diversity in the two breeds. However, Nei's gene diversity and Shannon index estimation was observed almost two folds in native cattle compared to Holstein breed. Less levels of diversity in Holstein cattle may be because of applying intensive selection programs. Conversely, native cattle have been less affected by selection. Therefore, it seems that Mazandaranian native cattle probably are better for breeding programs than Holstein cattle. Results showed that ISSR Markers are reliable and can be used in genetic diversity investigations.

[Allelic polymorphism of kappa-casein gene (CSN3) in Russian cattle breeds and its informative value as a genetic marker].

The frequencies of the kappa-casein gene (CSN3) alleles and genotypes have been determined in five Russian cattle breeds (Bestuzhev, Kalmyk, Russian Black Pied, Yaroslavl, and Yakut breeds) by means of PCR-RFLP analysis using two independent restriction nucleases (HinfI and TaqI) and by allele-specific PCR. Typing alleles A and B of CSN3 is of practical importance, because allele B is correlated with commercially valuable parameters of milk productivity (protein content and milk yield) and improves the cheese yielding capacity. The frequencies of the B allele of CSN3 in the breeds studied vary from 0.16 to 0.50; and those of the AB and BB genotypes, from 0.27 to 0.60 and from 0.02 to 0.23, respectively. The Yaroslavl breed had the highest frequencies of CSN3 allele B and genotype BB (0.50 and 0.23, respectively). The frequencies of the B allele and BB genotype in other breeds studied varied from 0.25 to 0.32 and from 0.03 to 0.09, respectively. In none of the breeds studied have the observed and expected heterozygosities been found to differ from each other significantly. However, the observed genotype distributions significantly differ from the expected one in some herds (in most such cases, an excess of heterozygotes is observed). Two herds of the Yaroslavl breed dramatically differ from each other in the heterozygosity level: a deficit (D = -0.14) and an excess (D = 0.20) of heterozygotes have been observed at the Mikhailovskoe and Gorshikha farms, respectively. In general, however, the heterozygosity of the Yaroslavl breed corresponds to the expected level (D = 0.04). Analysis of breeds for homogeneity with the use of Kulback's test has shown that all cattle breeds studied are heterogeneous, the CSN3 diversity within breeds being higher than that among different breeds, which is confirmed by low Fst values (0.0025-0.0431). Thus, a DNA marker based on CSN3 gene polymorphism is extremely important for breeding practice as a marker of milk quality; however, it is inapplicable to marking differences between breeds or phylogenetic relationships between cattle breeds because of the high diversity with respect to this locus within breeds.